My Bibliography

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Janakaloti Narayanareddy BR, Allipeta NR, Allard J, Gross SP. A new method to experimentally quantify dynamics of initial protein-protein interactions. Commun Biol. 2024 Mar 12;7(1):311. doi: 10.1038/s42003-024-05914-2. PubMed PMID: 38472292; PubMed Central PMCID: PMC10933273.

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Nguyen T, Narayanareddy BJ, Gross SP, Miles CE. ADP release can explain spatially-dependent kinesin binding times. bioRxiv. 2023 Nov 10;. doi: 10.1101/2023.11.08.563482. PubMed PMID: 37986962; PubMed Central PMCID: PMC10659338.

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Park S, Kim H, Wang Y, Eom DS, Allard J. Zebrafish airinemes optimize their shape between ballistic and diffusive search. Elife. 2022 Apr 25;11. doi: 10.7554/eLife.75690. PubMed PMID: 35467525; PubMed Central PMCID: PMC9098217.

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Goyette J, Depoil D, Yang Z, Isaacson SA, Allard J, van der Merwe PA, Gaus K, Dustin ML, Dushek O. Dephosphorylation accelerates the dissociation of ZAP70 from the T cell receptor. Proc Natl Acad Sci U S A. 2022 Mar 1;119(9). doi: 10.1073/pnas.2116815119. PubMed PMID: 35197288; PubMed Central PMCID: PMC8892339.

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Clemens L, Kutuzov M, Bayer KV, Goyette J, Allard J, Dushek O. Determination of the molecular reach of the protein tyrosine phosphatase SHP-1. Biophys J. 2021 May 18;120(10):2054-2066. doi: 10.1016/j.bpj.2021.03.019. Epub 2021 Mar 27. PubMed PMID: 33781765; PubMed Central PMCID: PMC8204385.

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Bovyn M, Janakaloti Narayanareddy BR, Gross S, Allard J. Diffusion of kinesin motors on cargo can enhance binding and run lengths during intracellular transport. Mol Biol Cell. 2021 Apr 19;32(9):984-994. doi: 10.1091/mbc.E20-10-0658. Epub 2021 Jan 13. PubMed PMID: 33439674; PubMed Central PMCID: PMC8108528.

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Clemens L, Dushek O, Allard J. Intrinsic Disorder in the T Cell Receptor Creates Cooperativity and Controls ZAP70 Binding. Biophys J. 2021 Jan 19;120(2):379-392. doi: 10.1016/j.bpj.2020.11.2266. Epub 2020 Dec 5. PubMed PMID: 33285117; PubMed Central PMCID: PMC7840419.

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Paoletti F, El-Sagheer AH, Allard J, Brown T, Dushek O, Esashi F. Molecular flexibility of DNA as a key determinant of RAD51 recruitment. EMBO J. 2020 Apr 1;39(7):e103002. doi: 10.15252/embj.2019103002. Epub 2020 Jan 14. PubMed PMID: 31943278; PubMed Central PMCID: PMC7110135.

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Zhang Y, Clemens L, Goyette J, Allard J, Dushek O, Isaacson SA. The Influence of Molecular Reach and Diffusivity on the Efficacy of Membrane-Confined Reactions. Biophys J. 2019 Oct 1;117(7):1189-1201. doi: 10.1016/j.bpj.2019.08.023. Epub 2019 Aug 28. PubMed PMID: 31543263; PubMed Central PMCID: PMC6818170.

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Allard J, Doumic M, Mogilner A, Oelz D. Bidirectional sliding of two parallel microtubules generated by multiple identical motors. J Math Biol. 2019 Jul;79(2):571-594. doi: 10.1007/s00285-019-01369-w. Epub 2019 Apr 23. PubMed PMID: 31016335; PubMed Central PMCID: PMC11100485.

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Liu K, Lowengrub J, Allard J. Efficient simulation of thermally fluctuating biopolymers immersed in fluids on 1-micron, 1-second scales. J Comput Phys. 2019 Jun 1;386:248-263. doi: 10.1016/j.jcp.2018.12.039. Epub 2019 Feb 22. PubMed PMID: 31787778; PubMed Central PMCID: PMC6884323.

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Liu K, Chu B, Newby J, Read EL, Lowengrub J, Allard J. Hydrodynamics of transient cell-cell contact: The role of membrane permeability and active protrusion length. PLoS Comput Biol. 2019 Apr;15(4):e1006352. doi: 10.1371/journal.pcbi.1006352. eCollection 2019 Apr. PubMed PMID: 31022168; PubMed Central PMCID: PMC6504115.

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Chapman DE, Reddy BJN, Huy B, Bovyn MJ, Cruz SJS, Al-Shammari ZM, Han H, Wang W, Smith DS, Gross SP. Regulation of in vivo dynein force production by CDK5 and 14-3-3ε and KIAA0528. Nat Commun. 2019 Jan 16;10(1):228. doi: 10.1038/s41467-018-08110-z. PubMed PMID: 30651536; PubMed Central PMCID: PMC6335402.

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Wang M, Allard J, Haun JB. Extracting multivalent detachment rates from heterogeneous nanoparticle populations. Phys Chem Chem Phys. 2018 Aug 22;20(33):21430-21440. doi: 10.1039/c8cp03118e. PubMed PMID: 30087954.

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Muretta JM, Reddy BJN, Scarabelli G, Thompson AF, Jariwala S, Major J, Venere M, Rich JN, Willard B, Thomas DD, Stumpff J, Grant BJ, Gross SP, Rosenfeld SS. A posttranslational modification of the mitotic kinesin Eg5 that enhances its mechanochemical coupling and alters its mitotic function. Proc Natl Acad Sci U S A. 2018 Feb 20;115(8):E1779-E1788. doi: 10.1073/pnas.1718290115. Epub 2018 Feb 5. PubMed PMID: 29432173; PubMed Central PMCID: PMC5828613.

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Bergman JP, Bovyn MJ, Doval FF, Sharma A, Gudheti MV, Gross SP, Allard JF, Vershinin MD. Cargo navigation across 3D microtubule intersections. Proc Natl Acad Sci U S A. 2018 Jan 16;115(3):537-542. doi: 10.1073/pnas.1707936115. Epub 2018 Jan 2. PubMed PMID: 29295928; PubMed Central PMCID: PMC5776960.

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Raz-Ben Aroush D, Ofer N, Abu-Shah E, Allard J, Krichevsky O, Mogilner A, Keren K. Actin Turnover in Lamellipodial Fragments. Curr Biol. 2017 Oct 9;27(19):2963-2973.e14. doi: 10.1016/j.cub.2017.08.066. Epub 2017 Sep 28. PubMed PMID: 28966086; PubMed Central PMCID: PMC5679493.

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Reddy BJN, Tripathy S, Vershinin M, Tanenbaum ME, Xu J, Mattson-Hoss M, Arabi K, Chapman D, Doolin T, Hyeon C, Gross SP. Heterogeneity in kinesin function. Traffic. 2017 Oct;18(10):658-671. doi: 10.1111/tra.12504. Epub 2017 Sep 8. PubMed PMID: 28731566; PubMed Central PMCID: PMC11166478.

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Liu K, Marple GR, Allard J, Li S, Veerapaneni S, Lowengrub J. Dynamics of a multicomponent vesicle in shear flow. Soft Matter. 2017 May 21;13(19):3521-3531. doi: 10.1039/c6sm02452a. Epub 2017 Apr 25. PubMed PMID: 28440378; PubMed Central PMCID: PMC5505236.

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Iniguez A, Allard J. Spatial pattern formation in microtubule post-translational modifications and the tight localization of motor-driven cargo. J Math Biol. 2017 Apr;74(5):1059-1080. doi: 10.1007/s00285-016-1053-x. Epub 2016 Sep 3. PubMed PMID: 27592217; PubMed Central PMCID: PMC6606455.

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Goyette J, Salas CS, Coker-Gordon N, Bridge M, Isaacson SA, Allard J, Dushek O. Biophysical assay for tethered signaling reactions reveals tether-controlled activity for the phosphatase SHP-1. Sci Adv. 2017 Mar;3(3):e1601692. doi: 10.1126/sciadv.1601692. eCollection 2017 Mar. PubMed PMID: 28378014; PubMed Central PMCID: PMC5365251.

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Barnhart EL, Allard J, Lou SS, Theriot JA, Mogilner A. Adhesion-Dependent Wave Generation in Crawling Cells. Curr Biol. 2017 Jan 9;27(1):27-38. doi: 10.1016/j.cub.2016.11.011. Epub 2016 Dec 8. PubMed PMID: 27939309; PubMed Central PMCID: PMC5225140.

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Bryant D, Clemens L, Allard J. Computational simulation of formin-mediated actin polymerization predicts homologue-dependent mechanosensitivity. Cytoskeleton (Hoboken). 2017 Jan;74(1):29-39. doi: 10.1002/cm.21344. Epub 2016 Nov 11. PubMed PMID: 27792274.

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Liu K, Hamilton C, Allard J, Lowengrub J, Li S. Wrinkling dynamics of fluctuating vesicles in time-dependent viscous flow. Soft Matter. 2016 Jun 29;12(26):5663-75. doi: 10.1039/c6sm00499g. PubMed PMID: 27136977; PubMed Central PMCID: PMC4927358.

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Mukhopadhyay H, de Wet B, Clemens L, Maini PK, Allard J, van der Merwe PA, Dushek O. Multisite Phosphorylation Modulates the T Cell Receptor ζ-Chain Potency but not the Switchlike Response. Biophys J. 2016 Apr 26;110(8):1896-1906. doi: 10.1016/j.bpj.2016.03.024. PubMed PMID: 27119648; PubMed Central PMCID: PMC4850346.

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Manakova K, Yan H, Lowengrub J, Allard J. Cell Surface Mechanochemistry and the Determinants of Bleb Formation, Healing, and Travel Velocity. Biophys J. 2016 Apr 12;110(7):1636-1647. doi: 10.1016/j.bpj.2016.03.008. PubMed PMID: 27074688; PubMed Central PMCID: PMC4833840.

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Newby J, Allard J. First-Passage Time to Clear the Way for Receptor-Ligand Binding in a Crowded Environment. Phys Rev Lett. 2016 Mar 25;116(12):128101. doi: 10.1103/PhysRevLett.116.128101. Epub 2016 Mar 21. PubMed PMID: 27058103.

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Lowengrub J, Allard J, Aland S. Numerical simulation of endocytosis: Viscous flow driven by membranes with non-uniformly distributed curvature-inducing molecules. J Comput Phys. 2016 Mar 15;309:112-128. doi: 10.1016/j.jcp.2015.12.055. PubMed PMID: 26869729; PubMed Central PMCID: PMC4746022.

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Lewis OL, Guy RD, Allard JF. Actin-myosin spatial patterns from a simplified isotropic viscoelastic model. Biophys J. 2014 Aug 19;107(4):863-70. doi: 10.1016/j.bpj.2014.06.041. PubMed PMID: 25140421; PubMed Central PMCID: PMC4142239.

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Gou J, Edelstein-Keshet L, Allard J. Mathematical model with spatially uniform regulation explains long-range bidirectional transport of early endosomes in fungal hyphae. Mol Biol Cell. 2014 Aug 15;25(16):2408-15. doi: 10.1091/mbc.E14-03-0826. Epub 2014 Jun 18. PubMed PMID: 24943842; PubMed Central PMCID: PMC4142613.

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Luo W, Yu CH, Lieu ZZ, Allard J, Mogilner A, Sheetz MP, Bershadsky AD. Analysis of the local organization and dynamics of cellular actin networks. J Cell Biol. 2013 Sep 30;202(7):1057-73. doi: 10.1083/jcb.201210123. PubMed PMID: 24081490; PubMed Central PMCID: PMC3787384.

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Danuser G, Allard J, Mogilner A. Mathematical modeling of eukaryotic cell migration: insights beyond experiments. Annu Rev Cell Dev Biol. 2013;29:501-28. doi: 10.1146/annurev-cellbio-101512-122308. Epub 2013 Jul 24. Review. PubMed PMID: 23909278; PubMed Central PMCID: PMC4148455.

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Allard J, Mogilner A. Traveling waves in actin dynamics and cell motility. Curr Opin Cell Biol. 2013 Feb;25(1):107-15. doi: 10.1016/j.ceb.2012.08.012. Epub 2012 Sep 15. Review. PubMed PMID: 22985541; PubMed Central PMCID: PMC3542403.

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Mogilner A, Allard J, Wollman R. Cell polarity: quantitative modeling as a tool in cell biology. Science. 2012 Apr 13;336(6078):175-9. doi: 10.1126/science.1216380. Review. PubMed PMID: 22499937.

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Allard JF, Dushek O, Coombs D, van der Merwe PA. Mechanical modulation of receptor-ligand interactions at cell-cell interfaces. Biophys J. 2012 Mar 21;102(6):1265-73. doi: 10.1016/j.bpj.2012.02.006. Epub 2012 Mar 20. PubMed PMID: 22455909; PubMed Central PMCID: PMC3309404.

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Cytrynbaum EN, Li YD, Allard JF, Mehrabian H. Estimating the bending modulus of a FtsZ bacterial-division protein filament. Phys Rev E Stat Nonlin Soft Matter Phys. 2012 Jan;85(1 Pt 1):011902. doi: 10.1103/PhysRevE.85.011902. Epub 2012 Jan 3. PubMed PMID: 22400586.

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Ambrose C, Allard JF, Cytrynbaum EN, Wasteneys GO. A CLASP-modulated cell edge barrier mechanism drives cell-wide cortical microtubule organization in Arabidopsis. Nat Commun. 2011 Aug 16;2:430. doi: 10.1038/ncomms1444. PubMed PMID: 21847104; PubMed Central PMCID: PMC3265373.

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Allard JF, Ambrose JC, Wasteneys GO, Cytrynbaum EN. A mechanochemical model explains interactions between cortical microtubules in plants. Biophys J. 2010 Aug 9;99(4):1082-90. doi: 10.1016/j.bpj.2010.05.037. PubMed PMID: 20712991; PubMed Central PMCID: PMC2920726.

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Allard JF, Wasteneys GO, Cytrynbaum EN. Mechanisms of self-organization of cortical microtubules in plants revealed by computational simulations. Mol Biol Cell. 2010 Jan 15;21(2):278-86. doi: 10.1091/mbc.e09-07-0579. Epub 2009 Nov 12. PubMed PMID: 19910489; PubMed Central PMCID: PMC2808237.

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Allard JF, Rutenberg AD. Pulling helices inside bacteria: imperfect helices and rings. Phys Rev Lett. 2009 Apr 17;102(15):158105. doi: 10.1103/PhysRevLett.102.158105. Epub 2009 Apr 17. PubMed PMID: 19518677.

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Allard JF, Cytrynbaum EN. Force generation by a dynamic Z-ring in Escherichia coli cell division. Proc Natl Acad Sci U S A. 2009 Jan 6;106(1):145-50. doi: 10.1073/pnas.0808657106. Epub 2008 Dec 29. PubMed PMID: 19114664; PubMed Central PMCID: PMC2629190.

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Allard JF, Hill AL, Rutenberg AD. Heterocyst patterns without patterning proteins in cyanobacterial filaments. Dev Biol. 2007 Dec 1;312(1):427-34. doi: 10.1016/j.ydbio.2007.09.045. Epub 2007 Sep 29. PubMed PMID: 17976569.

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Allard JF, Rutenberg AD. Steady-state helices of the actin homolog MreB inside bacteria: dynamics without motors. Phys Rev E Stat Nonlin Soft Matter Phys. 2007 Sep;76(3 Pt 1):031916. doi: 10.1103/PhysRevE.76.031916. Epub 2007 Sep 14. PubMed PMID: 17930280.